20201201_OS_radierant_orthologs

1 Plan

Repeat comparison but include bombyx.

Compare to d melanogaster. then also comapre across in both directiosns.

Look for overlaps.

require(magrittr)

## Loading required package: magrittr

require(tidyverse)

## Loading required package: tidyverse

## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──

## ✔ ggplot2 3.3.2     ✔ purrr   0.3.4
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## ✔ tidyr   1.1.2     ✔ stringr 1.4.0
## ✔ readr   1.4.0     ✔ forcats 0.5.0

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require(ShortRead)

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require(Herper)

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file.copy("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/BRC/obiroi/obiroi.fa", "obiroi.fa")
o_fa<-readFasta("obiroi.fa")

require(Herper)
export_CondaEnv("eggnog", yml_export= "eggnog_tom.yml", file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))
import_CondaEnv("eggnog_tom.yml", "eggnog", pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")

#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#external apps is not installed. this gives warning in build check. unclear why or if needed. 

Herper::with_CondaEnv("eggnog",system("ete3 build check"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")
Herper::with_CondaEnv("eggnog",system("ete3 ncbiquery -v 0"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")


#install_CondaTools("python=2.7","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)

#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)

# install_CondaTools(c("eggnog-mapper","ete3","ete_toolchain","ete3_external_apps"),"eggnog",channels="etetoolkit", pathToMiniConda= "/rugpfs/fs0/brc/scratch/mpaul/herper_conda/")
# install_CondaTools("ete3","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
# install_CondaTools("ete_toolchain","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)

read.delim("TC_ 20201201_Result/eggnogAnno_CondaVersionPy2_Scopeis50557_Targetis7227.emapper.annotations", skip = 3) %>% DT::datatable()

## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html

read.delim("TC_ 20201201_Result/eggnogAnno_WithPredictOrthp_CondaVersionPy2.emapper.predict_orthologs", skip = 3) %>% DT::datatable()

test <- read.delim("TC_ 20201201_Result/eggnogAnno_WithPredictOrthp_CondaVersionPy2.emapper.predict_orthologs")
nrow(test)

## [1] 727

# seed_ortholog just shows first 4 columns of the annotations result
# read.delim("TC_ 20201201_Result/eggnogAnno_CondaVersionPy2_Scopeis50557_Targetis7227.emapper.seed_orthologs", skip = 5) %>% DT::datatable()


#We are missing the orhtolog file 

Herper::with_CondaEnv("eggnog",system("python /rugpfs/fs0/brc/scratch/mpaul/eggnog/refactor-old/emapper.py -i /rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/BRC/obiroi/obiroi.fa --cpu 30 -m diamond --tax_scope 50557 --target_taxa 7227 --resume --data_dir /rugpfs/fs0/brc/scratch/tcarroll/autoProcessing//eggnogConda/dataDirConda/ --output  /rugpfs/fs0/brc/scratch/mpaul/1_kronauer/orli/Kronauer_Orli/20201201_OS_eggnog/eggnogAnno_refactor_Scopeis50557_Targetis7227"),pathToMiniConda=file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))

list_CondaPkgs("eggnog",pathToMiniConda=file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))

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## 64              pip           19.3.1   pkgs/main linux-64
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## 70            raxml           8.2.11  etetoolkit linux-64
## 71         readline              8.0   pkgs/main linux-64
## 72        reportlab           3.5.26   pkgs/main linux-64
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## 74       setuptools           44.0.0   pkgs/main linux-64
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##  date     2020-12-04                                 
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##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
## 
## [1] /rugpfs/fs0/brc/scratch/mpaul/software/R-4.0.3/library